UniProtKB/Swiss-Prot Q86Y38: Variant p.Arg406Trp

Xylosyltransferase 1
Gene: XYLT1
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Variant information Variant position:

406 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

LB/B The variants are classified into three categories: LP/P, LB/B and US.

LP/P: likely pathogenic or pathogenic.
LB/B: likely benign or benign.
US: uncertain significance

Residue change:

From Arginine (R) to Tryptophan (W) at position 406 (R406W, p.Arg406Trp). Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.
Physico-chemical properties:

Change from large size and basic (R) to large size and aromatic (W) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

-3 The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:

Lowest score: -4 (low probability of substitution).
Highest score: 11 (high probability of substitution).

More information can be found on the following page
Other resources:

Links to websites of interest for the variant.

Variant rs201009902 [ dbSNP | Ensembl ]

Sequence information Variant position:

406 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

959 The length of the canonical sequence.
Location on the sequence:

WRMATIWGGASLLSTYLQSM R DLLEMTDWPWDFFINLSAAD The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.
Residue conservation:

The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         WRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAAD

                              WRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAAD

Chimpanzee                    WRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAAD

Mouse                         WKMATIWGGASFLSTYLQSMRDLLEMTDWPWDFFINLSAAD

Sequence annotation in neighborhood:

The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:

Type: the type of sequence feature.
Positions: endpoints of the sequence feature.
Description: contains additional information about the feature.

Type	Positions	Description
Chain	1 – 959	Xylosyltransferase 1
Topological domain	39 – 959	Lumenal
Glycosylation	421 – 421	N-linked (GlcNAc...) asparagine
Disulfide bond	301 – 542
Helix	396 – 410

Literature citations
Polymorphisms in the xylosyltransferase genes cause higher serum XT-I activity in patients with pseudoxanthoma elasticum (PXE) and are involved in a severe disease course.
Schon S.; Schulz V.; Prante C.; Hendig D.; Szliska C.; Kuhn J.; Kleesiek K.; Gotting C.;
J. Med. Genet. 43:745-749(2006)
Cited for: INVOLVEMENT IN PXE; SUBCELLULAR LOCATION; VARIANT PXE SER-115; VARIANTS TRP-406 AND MET-665;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.